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Jin Y, Zhang X, Li H, Wu Z, Zhang W. High-rate partial nitritation as a pretreatment of anammox process. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:104592-104602. [PMID: 37707738 DOI: 10.1007/s11356-023-29663-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 08/30/2023] [Indexed: 09/15/2023]
Abstract
In this study, a laboratory-scale partial nitrification reactor (PN reactor) was used to treat high-ammonia-nitrogen wastewater, by changing the influent NH4+-N conversion rate as the main operating strategy, to investigate the upper limit of its NH4+-N conversion rate (ACR) and explore its feasibility as an anammox pre-process. During the experiment, PN reactor was successfully activated in only 10 days. The PN reactor reached the highest ACR value of approximately 10.24 kg N/(m3 · day) when the influent ACR was 16.57 kg N/(m3 · day), and the ammonia conversion efficiency (ACE) was 61.78% at this time. The ratio of [NO2--N]Eff/[NH4+-N]Eff was approximately 1.37 which was close to the theoretical ratio of 1.32. And feasibility exploration experiment proved that it was feasible to use this PN reactor as a pre-process of anammox. The PCR-DGGE results showed that the dominant phylum and genus in the reactor during the ACR experiment were Proteobacteria and Nitrosomonas, respectively. With the increase in the ACR, the relative concentration of Nitrosomonas sp. G1 increased from 15 to 40%. This indicates that its abundance is directly correlated with the increase in the ACR. High-throughput sequencing showed that increasing the ACR of the PN reactor greatly reduced the diversity and abundance of the system microbial community structure and changed the dominant phylum and genus; however, the stability of the system was not disrupted. High-throughput sequencing experiments showed that the abundance value of nitrosation enzymes accounted for 91.62%, which was positively correlated with the expression of nitrification genes in the genus Nitrosomonas.
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Affiliation(s)
- Yue Jin
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, 541004, China
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin, 541004, China
- College of Civil Engineering and Architecture, Guilin University of Technology, Guilin, 541004, China
| | - Xuli Zhang
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, 541004, China
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin, 541004, China
| | - Haixiang Li
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, 541004, China
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin, 541004, China
| | - Zhicheng Wu
- College of Civil Engineering and Architecture, Guilin University of Technology, Guilin, 541004, China
| | - Wenjie Zhang
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, 541004, China.
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin, 541004, China.
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Community Vertical Composition of the Laguna Negra Hypersaline Microbial Mat, Puna Region (Argentinean Andes). BIOLOGY 2022; 11:biology11060831. [PMID: 35741352 PMCID: PMC9220024 DOI: 10.3390/biology11060831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/20/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022]
Abstract
The Altiplano-Puna region is a high-altitude plateau in South America characterized by extreme conditions, including the highest UV incidence on Earth. The Laguna Negra is a hypersaline lake located in the Catamarca Province, northwestern Argentina, where stromatolites and other microbialites are found, and where life is mostly restricted to microbial mats. In this study, a particular microbial mat that covers the shore of the lake was explored, to unravel its layer-by-layer vertical structure in response to the environmental stressors therein. Microbial community composition was assessed by high-throughput 16S rRNA gene sequencing and pigment content analyses, complemented with microscopy tools to characterize its spatial arrangement within the mat. The top layer of the mat has a remarkable UV-tolerance feature, characterized by the presence of Deinococcus-Thermus and deinoxanthin, which might reflect a shielding strategy to cope with high UV radiation. Chloroflexi and Deltaproteobacteria were abundant in the second and third underlying layers, respectively. The bottom layer harbors copious Halanaerobiaeota. Subspherical aggregates composed of calcite, extracellular polymeric substances, abundant diatoms, and other microorganisms were observed all along the mat as the main structural component. This detailed study provides insights into the strategies of microbial communities to thrive under high UV radiation and hypersalinity in high-altitude lakes in the Altiplano-Puna region.
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Tian Z, Pu H, Cai D, Luo G, Zhao L, Li K, Zou J, Zhao X, Yu M, Wu Y, Yang T, Guo P, Hu X. Characterization of the bacterial microbiota in different gut and oral compartments of splendid japalure (Japalura sensu lato). BMC Vet Res 2022; 18:205. [PMID: 35624481 PMCID: PMC9137078 DOI: 10.1186/s12917-022-03300-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Gut and oral microbes form complex communities and play key roles in co-evolution with their hosts. However, little is understood about the bacterial community in lizards. Results In this study, we investigated the gut and oral bacterial communities in Japalura sensu lato from Sichuan Province, China, using 16S rRNA gene sequencing. Results showed that Bacteroidota (36.5%) and Firmicutes (32.8%) were the main phyla in the gut, while Proteobacteria, Bacteroidota, Firmicutes, and Actinobacteriota were the dominant phyla in the oral cavity. 16 S rRNA sequencing analysis of fecal samples showed that: (1) Bacteroidota was the most abundant in Japalura sensu lato, which was different from the bacterial community of insectivorous animals; (2) Bacteroidota, Firmicutes, Actinobacteriota, Fusobacteriota, and Cyanobacteria were the most abundant phylum in Japalura sensu lato. (3) Proteobacteria was the dominant phylum in Japalura sensu lato and other domestic insectivorous lizards (Shinisaurus crocodilurus, Phrynocephalus vlangalii, and Takydromus septentrionalis); (4) Comparing with the bacterial community of Shinisaurus crocodilurus, Phrynocephalus vlangalii, Takydromus septentrionalis, Liolaemus parvus, L. ruibali, and Phymaturus williamsi, Desulfobacterota was uniquely present in the gut of Japalura sensu lato. 16 S rRNA sequencing of oral samples showed that Chloroflexi and Deinococcota phyla were enriched in the oral cavity, which may have a significant influence on living in extreme environments. Conclusions Thus, based on 16 S rRNA sequencing analysis of the community composition of the gut and oral microbiomes, this study firstly represents a foundation for understanding the gut and oral microbial ecology of Japalura sensu lato, and constitutes a detail account of the diversity of the microbiota inhabiting the gut and oral cavity of Japalura sensu lato. Further researches will continue to reveal how gut and oral microbial communities may be impacting the ecology and evolution of lizards. Supplementary information The online version contains supplementary material available at 10.1186/s12917-022-03300-w.
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Affiliation(s)
- Zhige Tian
- Faculty of Agriculture, Forestry and Food Engineering, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin University, 644000, Yibin, People's Republic of China
| | - Hongli Pu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin University, 644000, Yibin, People's Republic of China
| | - Dongdong Cai
- Sichuan Animal Disease Control Central, 610000, Chengdu, People's Republic of China
| | - Guangmei Luo
- Faculty of Agriculture, Forestry and Food Engineering, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin University, 644000, Yibin, People's Republic of China
| | - Lili Zhao
- College of Veterinary Medicine, Jilin University, 130000, Changchun, People's Republic of China
| | - Ke Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin University, 644000, Yibin, People's Republic of China
| | - Jie Zou
- Faculty of Agriculture, Forestry and Food Engineering, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin University, 644000, Yibin, People's Republic of China
| | - Xiang Zhao
- Faculty of Agriculture, Forestry and Food Engineering, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin University, 644000, Yibin, People's Republic of China
| | - Min Yu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin University, 644000, Yibin, People's Republic of China
| | - Yayong Wu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin University, 644000, Yibin, People's Republic of China
| | - Tiankuo Yang
- Aviation Medical Appraisal Center, Civil Aviation Flight University of China, 618307, Guanghan, China.
| | - Peng Guo
- Faculty of Agriculture, Forestry and Food Engineering, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin University, 644000, Yibin, People's Republic of China.
| | - Xiaoliang Hu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin University, 644000, Yibin, People's Republic of China.
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Zhao T, Liu G, Liu D, Yi Y, Xie B, Liu H. Water recycle system in an artificial closed ecosystem - Lunar Palace 1: Treatment performance and microbial evolution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151370. [PMID: 34728198 DOI: 10.1016/j.scitotenv.2021.151370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
Water recycle systems have important implications to realize material circulation in biological regeneration life support systems, which is of significance for long-term space missions and future planetary base. Based on membrane biological activated carbon reactor (MBAR) technologies, the 'Lunar Palace 365' experiment established various treatment processes for condensate wastewater, domestic wastewater, urine, and used nutrient solutions. The 370-day operation data showed the CODMn index of purified condensate wastewater decreased to 0.74 ± 0.15 mg/L, which met the standards for drinking water quality. The average removal rate of organic contaminants in domestic wastewater by the MBAR was 85.7% ± 10.2%, and this MBAR also had a stable nitrification performance with effluent NO3--N concentrations fluctuating from 145.57 mg/L to 328.59 mg/L. Moreover, the purification of urine achieved the conversion of urea-N to NH4+-N and thus the partial recovery of nitrogen. 16S rDNA sequencing results revealed the evolution of microbial diversity and composition during the long-term operation. Meiothermus, Rhodanobacter, and Ochrobactrum were the dominant microorganisms in various MBARs.
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Affiliation(s)
- Ting Zhao
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100083, China; Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China
| | - Guanghui Liu
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100083, China; Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China
| | - Dianlei Liu
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100083, China; Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China
| | - Yue Yi
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Beizhen Xie
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100083, China; Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China.
| | - Hong Liu
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100083, China; Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China
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5
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Hardoim CCP, Ramaglia ACM, Lôbo-Hajdu G, Custódio MR. Community composition and functional prediction of prokaryotes associated with sympatric sponge species of southwestern Atlantic coast. Sci Rep 2021; 11:9576. [PMID: 33953214 PMCID: PMC8100286 DOI: 10.1038/s41598-021-88288-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 04/07/2021] [Indexed: 02/03/2023] Open
Abstract
Prokaryotes contribute to the health of marine sponges. However, there is lack of data on the assembly rules of sponge-associated prokaryotic communities, especially for those inhabiting biodiversity hotspots, such as ecoregions between tropical and warm temperate southwestern Atlantic waters. The sympatric species Aplysina caissara, Axinella corrugata, and Dragmacidon reticulatum were collected along with environmental samples from the north coast of São Paulo (Brazil). Overall, 64 prokaryotic phyla were detected; 51 were associated with sponge species, and the dominant were Proteobacteria, Bacteria (unclassified), Cyanobacteria, Crenarchaeota, and Chloroflexi. Around 64% and 89% of the unclassified operational taxonomical units (OTUs) associated with Brazilian sponge species showed a sequence similarity below 97%, with sequences in the Silva and NCBI Type Strain databases, respectively, indicating the presence of a large number of unidentified taxa. The prokaryotic communities were species-specific, ranging 56%-80% of the OTUs and distinct from the environmental samples. Fifty-four lineages were responsible for the differences detected among the categories. Functional prediction demonstrated that Ap. caissara was enriched for energy metabolism and biosynthesis of secondary metabolites, whereas D. reticulatum was enhanced for metabolism of terpenoids and polyketides, as well as xenobiotics' biodegradation and metabolism. This survey revealed a high level of novelty associated with Brazilian sponge species and that distinct members responsible from the differences among Brazilian sponge species could be correlated to the predicted functions.
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Affiliation(s)
- C C P Hardoim
- Institute of Biosciences, São Paulo State University, Coastal Campus of São Vicente, São Paulo, Brazil.
| | - A C M Ramaglia
- Institute of Biosciences, São Paulo State University, Coastal Campus of São Vicente, São Paulo, Brazil
| | - G Lôbo-Hajdu
- Department of Genetic, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - M R Custódio
- Department of Physiology, Center for Marine Biology, Biosciences Institute and NP-Biomar, São Paulo University, São Paulo, Brazil
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Zhu G, Huang S, Lu Y, Gu X. Simultaneous nitrification and denitrification in the bio-cathode of a multi-anode microbial fuel cell. ENVIRONMENTAL TECHNOLOGY 2021; 42:1260-1270. [PMID: 31538864 DOI: 10.1080/09593330.2019.1663938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
A multi-anode microbial fuel cell (MA-MFC) was developed to investigate simultaneous nitrification and denitrification (SND) in the bio-cathode. As the chemical oxygen demand to nitrogen (COD/N) ratio of the cathode was increased from 0 to 4.5, the electricity-producing quantity ranged between 498 and 543 C and the attained total nitrogen (TN) removal rate reached 12.07 g TN·m-3·d-1, resulting in a TN removal efficiency of 78.8% under the target COD/N ratio of 3.5. The removal of pollutants in series and parallel, open-circuit and closed-circuit were compared, respectively. The removal rates of TN, NH4+-N, and cathode and anode COD were all higher in the parallel connection configuration than in the series configuration. In parallel connection, the TN removal rate reached 14.4 g TN·m-3·d-1, which was 1.9 times that in series connection. Compared with the open-circuit system, the removal rate of TN in the closed-circuit system was improved by 17.8%, which could be ascribed to electrochemical denitrification. The results of high-throughput sequencing confirmed and clarified the presence of autotrophic denitrification and heterotrophic denitrification, including aerobic denitrification, when the MA-MFC had been operated for 18 months.
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Affiliation(s)
- Guangcan Zhu
- School of Energy and Environment, Southeast University, Nanjing, People's Republic of China
- State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, People's Republic of China
| | - Shan Huang
- School of Energy and Environment, Southeast University, Nanjing, People's Republic of China
- State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, People's Republic of China
| | - Yongze Lu
- School of Energy and Environment, Southeast University, Nanjing, People's Republic of China
- State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, People's Republic of China
| | - Xia Gu
- School of Energy and Environment, Southeast University, Nanjing, People's Republic of China
- State Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, People's Republic of China
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7
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Wang JM, Gan XM, Pu FJ, Wang WX, Ma M, Sun LL, Hu JW, Hu B, Zhang RP, Bai LL, Li L, Liu HH. Effect of fermentation bed on bacterial growth in the fermentation mattress material and cecum of ducks. Arch Microbiol 2021; 203:1489-1497. [PMID: 33398398 DOI: 10.1007/s00203-020-02145-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 11/11/2020] [Accepted: 12/03/2020] [Indexed: 11/29/2022]
Abstract
The composition of microorganisms in the gastrointestinal tract is closely related to the intestinal microenvironments and the exterior growth environments of host. In this study, 16S rDNA sequencing technology was adopted to investigate the influence of fermentation bed on the cecum microorganisms of ducks. Two feeding density treatment groups were set up, including group A (n = 4brids/m2) and group B (n = 6brids/m2). Samples were collected from the intermediate core fermentation layer (10-20 cm) of the fermented mattress materials and from the intestinal contents of ducks at 4, 6 and 8 weeks, respectively. Results showed that Bacteroidetes (20.12-27.17%) and Ruminococcaceae UCG-014 (2.97-10.1%) were the predominant microorganisms in duck cecum, while the Truepera (5.08-6.29%), Pricia (4.44-5.44%) and Luteimonas (3.62-4.99%) were the dominant microorganisms in fermentation mattress material. The cecum bacteria exhibited great difference among different growth periods of the ducks. Increasing the stocking density of ducks had a negative effect on the beneficial bacteria in the cecum. The microbial populations in fermentation mattress material were very different from that in the cecal. In summary, our findings can provide a scientific data for the rational use of fermentation bed feeding mode in poultry production.
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Affiliation(s)
- Jian- Mei Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Xin- Meng Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Fa-Jun Pu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Wan- Xia Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Min Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Ling-Li Sun
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Ji-Wei Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Bo Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Rong-Ping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Li-Li Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - He-He Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China.
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Park JH, Park JH, Lee SH, Jung SP, Kim SH. Enhancing anaerobic digestion for rural wastewater treatment with granular activated carbon (GAC) supplementation. BIORESOURCE TECHNOLOGY 2020; 315:123890. [PMID: 32731160 DOI: 10.1016/j.biortech.2020.123890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Notwithstanding many efforts to increase the efficiency of anaerobic digestion at low-temperature (winter) conditions, a cost-effective and efficient method is lacking. This study proposes a low-cost method of low-temperature (<35 °C) anaerobic digestion of wastewater, involving supplementation with granular activated carbon (GAC). Supplementation with GAC was found to reduce the lag time by 29.8% (from 15.1 to 10.6 days) and increase the maximum methane production rate by 23.4% (from 6.4 to 7.9 mL/day) at 25 °C. Network analysis demonstrated a strong co-occurrence of Syntrophobacteriales and hydrogenotrophic methanogens (Methanobacteriaceae; WSA2; Methanoregulaceae). GAC supplementation can drastically reduce the time required for organic matter decomposition and methane production, thereby increase the efficiency of wastewater treatment.
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Affiliation(s)
- Jeong-Hoon Park
- Sustainable Technology and Wellness R&D Group, Korea Institute of Industrial Technology (KITECH), Jeju-si 63243, Republic of Korea
| | - Jong-Hun Park
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Sang-Hoon Lee
- Department of Civil, Environmental and Architectural Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Sokhee P Jung
- Department of Environment and Energy Engineering, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sang-Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea.
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The Saltpan Microbiome is Structured by Sediment Depth and Minimally Influenced by Variable Hydration. Microorganisms 2020; 8:microorganisms8040538. [PMID: 32276533 PMCID: PMC7232383 DOI: 10.3390/microorganisms8040538] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/02/2020] [Accepted: 04/06/2020] [Indexed: 11/24/2022] Open
Abstract
Saltpans are a class of ephemeral wetland characterized by alternating periods of inundation, rising salinity, and desiccation. We obtained soil cores from a saltpan on the Mississippi Gulf coast in both the inundated and desiccated state. The microbiomes of surface and 30 cm deep sediment were determined using Illumina sequencing of the V4 region of the 16S rRNA gene. Bacterial and archaeal community composition differed significantly between sediment depths but did not differ between inundated and desiccated states. Well-represented taxa included marine microorganisms as well as multiple halophiles, both observed in greater proportions in surface sediment. Functional inference of metagenomic data showed that saltpan sediments in the inundated state had greater potential for microbial activity and that several energetic and degradation pathways were more prevalent in saltpan sediment than in nearby tidal marsh sediment. Microbial communities within saltpan sediments differed in composition from those in adjacent freshwater and brackish marshes. These findings indicate that the bacterial and archaeal microbiomes of saltpans are highly stratified by sediment depth and are only minimally influenced by changes in hydration. The surface sediment community is likely isolated from the shallow subsurface community by compaction, with the microbial community dominated by marine and terrestrial halophiles.
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Aesthetic Alteration of Marble Surfaces Caused by Biofilm Formation: Effects of Chemical Cleaning. COATINGS 2020. [DOI: 10.3390/coatings10020122] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite the massive presence of biofilms causing aesthetic alteration to the façade of the Monza Cathedral, our team in a previous work proved that the biocolonization was not a primary damaging factor if compared to chemical-physical deterioration due to the impact of air pollution. Nonetheless, the conservators tried to remove the sessile dwelling microorganisms to reduce discolouration. In this research, two nearby sculpted leaves made of Candoglia marble were selected to study the effects of a chemical treatment combining the biocides benzalkonium chloride, hydrogen peroxide and Algophase® and mechanical cleaning procedures. One leaf was cleaned with the biocides and mechanically, and the other was left untreated as control. The impact of the treatment was investigated after 1 month from the cleaning by digital microscopy, environmental scanning electron microscopy, confocal microscopy and molecular methods to determine the composition and the functional profiles of the bacterial communities. Despite the acceptable aesthetic results obtained, the overall cleaning treatment was only partially effective in removing the biofilm from the colonized surfaces and, therefore, not adequately suitable for the specific substrate. Furthermore, the cleaning process selected microorganisms potentially more resistant to biocides so that the efficacy of future re-treatment by antimicrobial agents could be negatively affected.
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Molina‐Menor E, Tanner K, Vidal‐Verdú À, Peretó J, Porcar M. Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea-land transition. Microb Biotechnol 2019; 12:1359-1370. [PMID: 31562755 PMCID: PMC6801134 DOI: 10.1111/1751-7915.13475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/29/2022] Open
Abstract
Microbial communities from harsh environments hold great promise as sources of biotechnologically relevant strains and compounds. In the present work, we have characterized the microorganisms from the supralittoral and splash zone in three different rocky locations of the Western Mediterranean coast, a tough environment characterized by high levels of irradiation and large temperature and salinity fluctuations. We have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. All three locations displayed very similar taxonomic profiles, with the genus Rubrobacter and the families Xenococcaceae, Flammeovirgaceae, Phyllobacteriaceae, Rhodobacteraceae and Trueperaceae being the most abundant taxa; and Ascomycota and halotolerant archaea as members of the eukaryotic and archaeal community respectively. In parallel, the culture-dependent approach yielded a 100-isolates collection, out of which 12 displayed high antioxidant activities, as evidenced by two in vitro (hydrogen peroxide and DPPH) and confirmed in vivo with Caenorhabditis elegans assays, in which two isolates, CR22 and CR24, resulted in extended survival rates of the nematodes. This work is the first complete characterization of the Mediterranean splash-zone coastal microbiome, and our results indicate that this microbial niche is home of an extremophilic community that holds biotechnological potential.
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Affiliation(s)
- Esther Molina‐Menor
- Institute for Integrative Systems Biology ISysBioUniversitat de València‐CSICPaterna46980Spain
| | - Kristie Tanner
- Institute for Integrative Systems Biology ISysBioUniversitat de València‐CSICPaterna46980Spain
- Darwin Bioprospecting Excellence S.L. Parc Científic Universitat de ValènciaPaterna46980Spain
| | - Àngela Vidal‐Verdú
- Institute for Integrative Systems Biology ISysBioUniversitat de València‐CSICPaterna46980Spain
| | - Juli Peretó
- Institute for Integrative Systems Biology ISysBioUniversitat de València‐CSICPaterna46980Spain
- Darwin Bioprospecting Excellence S.L. Parc Científic Universitat de ValènciaPaterna46980Spain
- Departament de Bioquímica i Biologia MolecularUniversitat de ValènciaBurjassot46100Spain
| | - Manuel Porcar
- Institute for Integrative Systems Biology ISysBioUniversitat de València‐CSICPaterna46980Spain
- Darwin Bioprospecting Excellence S.L. Parc Científic Universitat de ValènciaPaterna46980Spain
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12
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Engineered Passive Potassium Conductance in the KR2 Sodium Pump. Biophys J 2019; 116:1941-1951. [PMID: 31036257 DOI: 10.1016/j.bpj.2019.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/31/2019] [Accepted: 04/03/2019] [Indexed: 11/23/2022] Open
Abstract
Light-driven sodium pumps (NaRs) are microbial rhodopsins that utilize light energy to actively transport sodium ions out of the cell. Here, we used targeted mutagenesis and electrophysiological methods in living cells to demonstrate that NaRs can be converted into light-activated cation channels by molecular engineering. Specifically, introduction of the R109Q mutation into the sodium ion pump of Dokdonia eikasta (KR2) results in passive ion conductance, with a high preference for potassium over sodium ions. However, in this mutant, residual active outward pumping of sodium ions competes with passive inward transport of potassium. Channel-like behavior could also be achieved by introduction of other mutations into the KR2 counterion complex, and further, these modifications were transferrable to other NaRs. Combining the R109Q replacement with modifications at position S70 removed the residual sodium pumping and greatly enhanced the channel-like activity. However, passive photocurrents were only observed in leak mutants if the KR2 counterions, D116 and D251, were deprotonated, which was only observed under alkaline conditions. Overall, our results reveal that interactions between R109 and the nearby residues, L75, S70, D116, and D251, prevent passive backflow during ion transport in NaRs.
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13
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Li L, Qian G, Ye L, Hu X, Yu X, Lyu W. Research on the enhancement of biological nitrogen removal at low temperatures from ammonium-rich wastewater by the bio-electrocoagulation technology in lab-scale systems, pilot-scale systems and a full-scale industrial wastewater treatment plant. WATER RESEARCH 2018; 140:77-89. [PMID: 29698857 DOI: 10.1016/j.watres.2018.04.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/23/2018] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
In cold areas, nitrogen removal performance of wastewater treatment plants (WWTP) declines greatly in winter. This paper systematically describes the enhancement effect of a periodic reverse electrocoagulation technology on biological nitrogen removal at low temperatures. The study showed that in the lab-scale systems, the electrocoagulation technology improved the biomass amount, enzyme activity and the amount of nitrogen removal bacteria (Nitrosomonas, Nitrobacter, Paracoccus, Thauera and Enterobacter). This enhanced nitrification and denitrification of activated sludge at low temperatures. In the pilot-scale systems, the electrocoagulation technology increased the relative abundance of cold-adapted microorganisms (Luteimonas and Trueperaceae) at low temperatures. In a full-scale industrial WWTP, comparison of data from winter 2015 and winter 2016 showed that effluent chemical oxygen demand (COD), NH4+-N, and NO3--N reduced by 10.37, 3.84, and 136.43 t, respectively, throughout the winter, after installation of electrocoagulation devices. These results suggest that the electrocoagulation technology is able to improve the performance of activated sludge under low-temperature conditions. This technology provides a new way for upgrading of the performance of WWTPs in cold areas.
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Affiliation(s)
- Liang Li
- School of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - Guangsheng Qian
- School of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China.
| | - Linlin Ye
- School of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - Xiaomin Hu
- School of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - Xin Yu
- School of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - Weijian Lyu
- School of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
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14
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Biochemical characterization of a highly thermostable amylosucrase from Truepera radiovictrix DSM 17093. Int J Biol Macromol 2018; 116:744-752. [DOI: 10.1016/j.ijbiomac.2018.05.096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 12/31/2022]
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15
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Aanderud ZT, Saurey S, Ball BA, Wall DH, Barrett JE, Muscarella ME, Griffin NA, Virginia RA, Barberán A, Adams BJ. Stoichiometric Shifts in Soil C:N:P Promote Bacterial Taxa Dominance, Maintain Biodiversity, and Deconstruct Community Assemblages. Front Microbiol 2018; 9:1401. [PMID: 30018601 PMCID: PMC6037766 DOI: 10.3389/fmicb.2018.01401] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/07/2018] [Indexed: 11/13/2022] Open
Abstract
Imbalances in C:N:P supply ratios may cause bacterial resource limitations and constrain biogeochemical processes, but the importance of shifts in soil stoichiometry are complicated by the nearly limitless interactions between an immensely rich species pool and a multiple chemical resource forms. To more clearly identify the impact of soil C:N:P on bacteria, we evaluated the cumulative effects of single and coupled long-term nutrient additions (i.e., C as mannitol, N as equal concentrations NH4+ and NO3-, and P as Na3PO4) and water on communities in an Antarctic polar desert, Taylor Valley. Untreated soils possessed relatively low bacterial diversity, simplified organic C sources due to the absence of plants, limited inorganic N, and excess soil P potentially attenuating links between C:N:P. After 6 years of adding resources, an alleviation of C and N colimitation allowed one rare Micrococcaceae, an Arthrobacter species, to dominate, comprising 47% of the total community abundance and elevating soil respiration by 136% relative to untreated soils. The addition of N alone reduced C:N ratios, elevated bacterial richness and diversity, and allowed rare taxa relying on ammonium and nitrite for metabolism to become more abundant [e.g., nitrite oxidizing Nitrospira species (Nitrosomonadaceae), denitrifiers utilizing nitrite (Gemmatimonadaceae) and members of Rhodobacteraceae with a high affinity for ammonium]. Based on community co-occurrence networks, lower C:P ratios in soils following P and CP additions created more diffuse and less connected communities by disrupting 73% of species interactions and selecting for taxa potentially exploiting abundant P. Unlike amended nutrients, water additions alone elicited no lasting impact on communities. Our results suggest that as soils become nutrient rich a wide array of outcomes are possible from species dominance and the deconstruction of species interconnectedness to the maintenance of biodiversity.
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Affiliation(s)
- Zachary T. Aanderud
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Sabrina Saurey
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Becky A. Ball
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States
| | - Diana H. Wall
- Department of Biology, School of Global Environmental Sustainability, Colorado State University, Fort Collins, CO, United States
| | - John E. Barrett
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA, United States
| | - Mario E. Muscarella
- Department of Plant Biology, University of Illinois Urbana-Champaign, Champaign, IL, United States
| | - Natasha A. Griffin
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Ross A. Virginia
- Environmental Studies Program, Dartmouth College, Hanover, NH, United States
| | - Albert Barberán
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Byron J. Adams
- Evolutionary Ecology Laboratories, and Monte L. Bean Museum, Department of Biology, Brigham Young University, Provo, UT, United States
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16
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Alessi AM, Bird SM, Oates NC, Li Y, Dowle AA, Novotny EH, deAzevedo ER, Bennett JP, Polikarpov I, Young JPW, McQueen-Mason SJ, Bruce NC. Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:166. [PMID: 29946357 PMCID: PMC6004670 DOI: 10.1186/s13068-018-1164-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/05/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Lignocellulose is one of the most abundant forms of fixed carbon in the biosphere. Current industrial approaches to the degradation of lignocellulose employ enzyme mixtures, usually from a single fungal species, which are only effective in hydrolyzing polysaccharides following biomass pre-treatments. While the enzymatic mechanisms of lignocellulose degradation have been characterized in detail in individual microbial species, the microbial communities that efficiently breakdown plant materials in nature are species rich and secrete a myriad of enzymes to perform "community-level" metabolism of lignocellulose. Single-species approaches are, therefore, likely to miss important aspects of lignocellulose degradation that will be central to optimizing commercial processes. RESULTS Here, we investigated the microbial degradation of wheat straw in liquid cultures that had been inoculated with wheat straw compost. Samples taken at selected time points were subjected to multi-omics analysis with the aim of identifying new microbial mechanisms for lignocellulose degradation that could be applied in industrial pre-treatment of feedstocks. Phylogenetic composition of the community, based on sequenced bacterial and eukaryotic ribosomal genes, showed a gradual decrease in complexity and diversity over time due to microbial enrichment. Taxonomic affiliation of bacterial species showed dominance of Bacteroidetes and Proteobacteria and high relative abundance of genera Asticcacaulis, Leadbetterella and Truepera. The eukaryotic members of the community were enriched in peritrich ciliates from genus Telotrochidium that thrived in the liquid cultures compared to fungal species that were present in low abundance. A targeted metasecretome approach combined with metatranscriptomics analysis, identified 1127 proteins and showed the presence of numerous carbohydrate-active enzymes extracted from the biomass-bound fractions and from the culture supernatant. This revealed a wide array of hydrolytic cellulases, hemicellulases and carbohydrate-binding modules involved in lignocellulose degradation. The expression of these activities correlated to the changes in the biomass composition observed by FTIR and ssNMR measurements. CONCLUSIONS A combination of mass spectrometry-based proteomics coupled with metatranscriptomics has enabled the identification of a large number of lignocellulose degrading enzymes that can now be further explored for the development of improved enzyme cocktails for the treatment of plant-based feedstocks. In addition to the expected carbohydrate-active enzymes, our studies reveal a large number of unknown proteins, some of which may play a crucial role in community-based lignocellulose degradation.
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Affiliation(s)
- Anna M. Alessi
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Susannah M. Bird
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Nicola C. Oates
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Yi Li
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Adam A. Dowle
- Department of Biology, Bioscience Technology Facility, University of York, York, YO10 5DD UK
| | | | - Eduardo R. deAzevedo
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP Brazil
| | - Joseph P. Bennett
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Igor Polikarpov
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP Brazil
| | | | - Simon J. McQueen-Mason
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Neil C. Bruce
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
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17
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Wang X, Cao A, Zhao G, Zhou C, Xu R. Microbial community structure and diversity in a municipal solid waste landfill. WASTE MANAGEMENT (NEW YORK, N.Y.) 2017; 66:79-87. [PMID: 28442259 DOI: 10.1016/j.wasman.2017.04.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 04/05/2017] [Accepted: 04/09/2017] [Indexed: 05/21/2023]
Abstract
Municipal solid waste (MSW) landfills are the most prevalent waste disposal method and constitute one of the largest sources of anthropogenic methane emissions in the world. Microbial activities in disposed waste play a crucial role in greenhouse gas emissions; however, only a few studies have examined metagenomic microbial profiles in landfills. Here, the MiSeq high-throughput sequencing method was applied for the first time to examine microbial diversity of the cover soil and stored waste located at different depths (0-150cm) in a typical MSW landfill in Yangzhou City, East China. The abundance of microorganisms in the cover soil (0-30cm) was the lowest among all samples, whereas that in stored waste decreased from the top to the middle layer (30-90cm) and then increased from the middle to the bottom layer (90-150cm). In total, 14 phyla and 18 genera were found in the landfill. A microbial diversity analysis showed that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla, whereas Halanaerobium, Methylohalobius, Syntrophomonas, Fastidiosipila, and Spirochaeta were the dominant genera. Methylohalobius (methanotrophs) was more abundant in the cover layers of soil than in stored waste, whereas Syntrophomonas and Fastidiosipila, which affect methane production, were more abundant in the middle to bottom layers (90-150cm) in stored waste. A canonical correlation analysis showed that microbial diversity in the landfill was most strongly correlated with the conductivity, organic matter, and moisture content of the stored waste.
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Affiliation(s)
- Xiaolin Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Aixin Cao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guozhu Zhao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
| | - Chuanbin Zhou
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Rui Xu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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18
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Matrosova VY, Gaidamakova EK, Makarova KS, Grichenko O, Klimenkova P, Volpe RP, Tkavc R, Ertem G, Conze IH, Brambilla E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Daligault H, Davenport K, Erkkila T, Goodwin LA, Gu W, Munk C, Teshima H, Xu Y, Chain P, Woolbert M, Gunde-Cimerman N, Wolf YI, Grebenc T, Gostinčar C, Daly MJ. High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460. Stand Genomic Sci 2017; 12:46. [PMID: 28775794 PMCID: PMC5534035 DOI: 10.1186/s40793-017-0258-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/20/2017] [Indexed: 11/24/2022] Open
Abstract
The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS 0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been studied since 1987, first under the name Deinobacter grandis, then Deinococcus grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC content and 3894 predicted genes) divided into six genome partitions, five of which are confirmed to be circular. Circularity was determined manually by mate pair linkage. Approximately 76% of the predicted proteins contained identifiable Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79% and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus geothermalis DSM 11300, respectively. The most striking differences between D. ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in nitrogen metabolism, including nitrate and nitrite reductases, that D. radiodurans lacks. Moreover, genes previously considered to be important to IR resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp, and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage.
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Affiliation(s)
- Vera Y. Matrosova
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Elena K. Gaidamakova
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD USA
| | - Olga Grichenko
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Polina Klimenkova
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Robert P. Volpe
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Rok Tkavc
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Gözen Ertem
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
| | - Isabel H. Conze
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- University of Bielefeld, Bielefeld, Germany
| | - Evelyne Brambilla
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Alicia Clum
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Manoj Pillay
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | | | - TBK Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | | | - Wei Gu
- Los Alamos National Laboratory, Los Alamos, NM USA
| | | | | | - Yan Xu
- Los Alamos National Laboratory, Los Alamos, NM USA
| | | | - Michael Woolbert
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD USA
| | - Tine Grebenc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michael J. Daly
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
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Toneatti DM, Albarracín VH, Flores MR, Polerecky L, Farías ME. Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites. Front Microbiol 2017; 8:646. [PMID: 28446906 PMCID: PMC5388776 DOI: 10.3389/fmicb.2017.00646] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/29/2017] [Indexed: 11/13/2022] Open
Abstract
At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community. We herein discussed how, in only 7 mm, a drastic succession of metabolic adaptations occurred: i.e., microbial communities shift from a UV-high/oxic world to an IR-low/anoxic/high H2S environment which force stratification and metabolic specialization of the bacterial community, thus, modulating the chemical faces of the Socompa stromatolites. The oxic zone was dominated by Deinococcus sp. at top surface (0.3 mm), followed by a second layer of Coleofasciculus sp. (0.3 to ∼2 mm). Sequences from anoxygenic phototrophic Alphaproteobacteria, along with an increasing diversity of phyla including Bacteroidetes, Spirochaetes were found at middle layers 3 and 4. Deeper layers (5–7 mm) were mostly occupied by sulfate reducers of Deltaproteobacteria, Bacteroidetes and Firmicutes, next to a high diversity and equitable community of rare, unclassified and candidate phyla. This analysis showed how microbial communities stratified in a physicochemical vertical profile and according to the light source. It also gives an insight of which bacterial metabolic capabilities might operate and produce a microbial cooperative strategy to thrive in one of the most extreme environments on Earth.
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Affiliation(s)
- Diego M Toneatti
- Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico - Consejo Nacional de Investigaciones Científicas y TécnicasSan Miguel de Tucumán, Argentina
| | - Virginia H Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico - Consejo Nacional de Investigaciones Científicas y TécnicasSan Miguel de Tucumán, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de TucumánSan Miguel de Tucumán, Argentina.,Centro Integral de Microscopía Electrónica, Centro Científico Tecnológico - Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de TucumánSan Miguel de Tucumán, Argentina
| | - Maria R Flores
- Department of Earth Sciences - Geochemistry, Utrecht UniversityUtrecht, Netherlands
| | - Lubos Polerecky
- Department of Earth Sciences - Geochemistry, Utrecht UniversityUtrecht, Netherlands
| | - María E Farías
- Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico - Consejo Nacional de Investigaciones Científicas y TécnicasSan Miguel de Tucumán, Argentina
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20
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Rahman SF, Kantor RS, Huddy R, Thomas BC, van Zyl AW, Harrison STL, Banfield JF. Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings. Microbiologyopen 2017; 6. [PMID: 28215046 PMCID: PMC5458468 DOI: 10.1002/mbo3.446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/19/2016] [Indexed: 11/13/2022] Open
Abstract
Thiocyanate (SCN−) is a toxic compound that forms when cyanide (CN−), used to recover gold, reacts with sulfur species. SCN−‐degrading microbial communities have been studied, using bioreactors fed synthetic wastewater. The inclusion of suspended solids in the form of mineral tailings, during the development of the acclimatized microbial consortium, led to the selection of an active planktonic microbial community. Preliminary analysis of the community composition revealed reduced microbial diversity relative to the laboratory‐based reactors operated without suspended solids. Despite minor upsets during the acclimation period, the SCN− degradation performance was largely unchanged under stable operating conditions. Here, we characterized the microbial community in the SCN− degrading bioreactor that included solid particulate tailings and determined how it differed from the biofilm‐based communities in solids‐free reactor systems inoculated from the same source. Genome‐based analysis revealed that the presence of solids decreased microbial diversity, selected for different strains, suppressed growth of thiobacilli inferred to be primarily responsible for SCN− degradation, and promoted growth of Trupera, an organism not detected in the reactors without solids. In the solids reactor community, heterotrophy and aerobic respiration represent the dominant metabolisms. Many organisms have genes for denitrification and sulfur oxidation, but only one Thiobacillus sp. in the solids reactor has SCN− degradation genes. The presence of the solids prevented floc and biofilm formation, leading to the observed reduced microbial diversity. Collectively the presence of the solids and lack of biofilm community may result in a process with reduced resilience to process perturbations, including fluctuations in the influent composition and pH. The results from this investigation have provided novel insights into the community composition of this industrially relevant community, giving potential for improved process control and operation through ongoing process monitoring.
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Affiliation(s)
- Sumayah F Rahman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Rose S Kantor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Robert Huddy
- Department of Chemical Engineering, Center for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Andries W van Zyl
- Department of Chemical Engineering, Center for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Susan T L Harrison
- Department of Chemical Engineering, Center for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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21
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Covino S, Fabianová T, Křesinová Z, Čvančarová M, Burianová E, Filipová A, Vořísková J, Baldrian P, Cajthaml T. Polycyclic aromatic hydrocarbons degradation and microbial community shifts during co-composting of creosote-treated wood. JOURNAL OF HAZARDOUS MATERIALS 2016; 301:17-26. [PMID: 26342147 DOI: 10.1016/j.jhazmat.2015.08.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 08/13/2015] [Accepted: 08/13/2015] [Indexed: 06/05/2023]
Abstract
The feasibility of decontaminating creosote-treated wood (CTW) by co-composting with agricultural wastes was investigated using two bulking agents, grass cuttings (GC) and broiler litter (BL), each employed at a 1:1 ratio with the matrix. The initial concentration of total polycyclic aromatic hydrocarbons (PAHs) in CTW (26,500 mg kg(-1)) was reduced to 3 and 19% after 240 d in GC and BL compost, respectively. PAH degradation exceeded the predicted bioaccesible threshold, estimated through sequential supercritical CO2 extraction, together with significant detoxification, assessed by contact tests using Vibrio fisheri and Hordeum vulgare. GC composting was characterized by high microbial biomass growth in the early phases, as suggested by phospholipid fatty acid analyses. Based on the 454-pyrosequencing results, fungi (mostly Saccharomycetales) constituted an important portion of the microbial community, and bacteria were characterized by rapid shifts (from Firmicutes (Bacilli) and Actinobacteria to Proteobacteria). However, during BL composting, larger amounts of prokaryotic and eukaryotic PLFA markers were observed during the cooling and maturation phases, which were dominated by Proteobacteria and fungi belonging to the Ascomycota and those putatively related to the Glomeromycota. This work reports the first in-depth analysis of the chemical and microbiological processes that occur during the co-composting of a PAH-contaminated matrix.
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Affiliation(s)
- Stefano Covino
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Institute of Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague 2, Czech Republic
| | - Tereza Fabianová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Zdena Křesinová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Monika Čvančarová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Eva Burianová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Alena Filipová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Institute of Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague 2, Czech Republic
| | - Jana Vořísková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Institute of Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague 2, Czech Republic.
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22
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From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization. Sci Rep 2015; 5:12978. [PMID: 26268667 PMCID: PMC4534789 DOI: 10.1038/srep12978] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/16/2015] [Indexed: 12/02/2022] Open
Abstract
Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil soluble Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera (typically Nocardioides and Altererythrobacter) were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes.
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23
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Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass. Appl Environ Microbiol 2014; 80:7423-32. [PMID: 25261509 DOI: 10.1128/aem.02795-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 09/19/2014] [Indexed: 12/14/2022] Open
Abstract
Microbial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of various compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic-liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX and IL pretreatment enhanced the deconstruction of the SG biomass approximately 2-fold. Two-dimensional nuclear magnetic resonance (2D-NMR) experiments and acetyl bromide-reactive-lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during microbial biomass deconstruction, and lignin remaining in the residual biomass was largely unmodified. Small-subunit (SSU) rRNA gene amplicon libraries revealed that although the dominant taxa across these chemical pretreatments were consistently represented by members of the Firmicutes, the Bacteroidetes, and Deinococcus-Thermus, the abundance of selected operational taxonomic units (OTUs) varied, suggesting adaptations to the different substrates. Combining the observations of differences in the community structure and the chemical and physical structure of the biomass, we hypothesize specific roles for individual community members in biomass deconstruction.
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24
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Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria. Proc Natl Acad Sci U S A 2014; 111:6732-7. [PMID: 24706784 DOI: 10.1073/pnas.1403051111] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Light-activated, ion-pumping rhodopsins are broadly distributed among many different bacteria and archaea inhabiting the photic zone of aquatic environments. Bacterial proton- or sodium-translocating rhodopsins can convert light energy into a chemiosmotic force that can be converted into cellular biochemical energy, and thus represent a widespread alternative form of photoheterotrophy. Here we report that the genome of the marine flavobacterium Nonlabens marinus S1-08(T) encodes three different types of rhodopsins: Nonlabens marinus rhodopsin 1 (NM-R1), Nonlabens marinus rhodopsin 2 (NM-R2), and Nonlabens marinus rhodopsin 3 (NM-R3). Our functional analysis demonstrated that NM-R1 and NM-R2 are light-driven outward-translocating H(+) and Na(+) pumps, respectively. Functional analyses further revealed that the light-activated NM-R3 rhodopsin pumps Cl(-) ions into the cell, representing the first chloride-pumping rhodopsin uncovered in a marine bacterium. Phylogenetic analysis revealed that NM-R3 belongs to a distinct phylogenetic lineage quite distant from archaeal inward Cl(-)-pumping rhodopsins like halorhodopsin, suggesting that different types of chloride-pumping rhodopsins have evolved independently within marine bacterial lineages. Taken together, our data suggest that similar to haloarchaea, a considerable variety of rhodopsin types with different ion specificities have evolved in marine bacteria, with individual marine strains containing as many as three functionally different rhodopsins.
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25
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Riedel T, Gómez-Consarnau L, Tomasch J, Martin M, Jarek M, González JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Göker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, Wagner-Döbler I. Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PLoS One 2013; 8:e57487. [PMID: 23526944 PMCID: PMC3587595 DOI: 10.1371/journal.pone.0057487] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/22/2013] [Indexed: 01/10/2023] Open
Abstract
Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition.
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Affiliation(s)
- Thomas Riedel
- Helmholtz-Centre for Infection Research, Braunschweig, Germany.
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26
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There are more small amino acids and fewer aromatic rings in proteins of ionizing radiation-resistant bacteria. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0612-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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27
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Yuan M, Chen M, Zhang W, Lu W, Wang J, Yang M, Zhao P, Tang R, Li X, Hao Y, Zhou Z, Zhan Y, Yu H, Teng C, Yan Y, Ping S, Wang Y, Lin M. Genome sequence and transcriptome analysis of the radioresistant bacterium Deinococcus gobiensis: insights into the extreme environmental adaptations. PLoS One 2012; 7:e34458. [PMID: 22470573 PMCID: PMC3314630 DOI: 10.1371/journal.pone.0034458] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Accepted: 03/01/2012] [Indexed: 12/04/2022] Open
Abstract
The desert is an excellent model for studying evolution under extreme environments. We present here the complete genome and ultraviolet (UV) radiation-induced transcriptome of Deinococcus gobiensis I-0, which was isolated from the cold Gobi desert and shows higher tolerance to gamma radiation and UV light than all other known microorganisms. Nearly half of the genes in the genome encode proteins of unknown function, suggesting that the extreme resistance phenotype may be attributed to unknown genes and pathways. D. gobiensis also contains a surprisingly large number of horizontally acquired genes and predicted mobile elements of different classes, which is indicative of adaptation to extreme environments through genomic plasticity. High-resolution RNA-Seq transcriptome analyses indicated that 30 regulatory proteins, including several well-known regulators and uncharacterized protein kinases, and 13 noncoding RNAs were induced immediately after UV irradiation. Particularly interesting is the UV irradiation induction of the phrB and recB genes involved in photoreactivation and recombinational repair, respectively. These proteins likely include key players in the immediate global transcriptional response to UV irradiation. Our results help to explain the exceptional ability of D. gobiensis to withstand environmental extremes of the Gobi desert, and highlight the metabolic features of this organism that have biotechnological potential.
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Affiliation(s)
- Menglong Yuan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
- College of Life Sciences, Beijing Normal University, Beijing, People's Republic of China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Wei Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Mingkun Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Peng Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Ran Tang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Xinna Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yanhua Hao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yuhua Zhan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Haiying Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Chao Teng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Shuzhen Ping
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yingdian Wang
- College of Life Sciences, Beijing Normal University, Beijing, People's Republic of China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
- * E-mail:
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28
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Pati A, Zhang X, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Hauser L, Jeffries CD, Brambilla EM, Röhl A, Mwirichia R, Rohde M, Tindall BJ, Sikorski J, Wirth R, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M. Complete genome sequence of Oceanithermus profundus type strain (506). Stand Genomic Sci 2011; 4:210-20. [PMID: 21677858 PMCID: PMC3111992 DOI: 10.4056/sigs.1734292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Oceanithermus, which belongs to the family Thermaceae. The genus currently comprises two species whose members are thermophilic and are able to reduce sulfur compounds and nitrite. The organism is adapted to the salinity of sea water, is able to utilize a broad range of carbohydrates, some proteinaceous substrates, organic acids and alcohols. This is the first completed genome sequence of a member of the genus Oceanithermus and the fourth sequence from the family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and 54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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29
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Pukall R, Zeytun A, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Deinococcus maricopensis type strain (LB-34). Stand Genomic Sci 2011; 4:163-72. [PMID: 21677853 PMCID: PMC3111983 DOI: 10.4056/sigs.1633949] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Deinococcus maricopensis (Rainey and da Costa 2005) is a member of the genus Deinococcus, which is comprised of 44 validly named species and is located within the deeply branching bacterial phylum Deinococcus-Thermus. Strain LB-34(T) was isolated from a soil sample from the Sonoran Desert in Arizona. Various species of the genus Deinococcus are characterized by extreme radiation resistance, with D. maricopensis being resistant in excess of 10 kGy. Even though the genomes of three Deinococcus species, D. radiodurans, D. geothermalis and D. deserti, have already been published, no special physiological characteristic is currently known that is unique to this group. It is therefore of special interest to analyze the genomes of additional species of the genus Deinococcus to better understand how these species adapted to gamma- or UV ionizing-radiation. The 3,498,530 bp long genome of D. maricopensis with its 3,301 protein-coding and 66 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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